Homo sapiens smoking data (GSE68559)

Run parameters

TestExpressioncutoffNormalisationVariancecutoffCoexpression_measureEdge_thresholdThreshold_method
GSE685591upper_quartile0.025pidc0.95empiricaldistzero

Data preprocessing

Data cleaning

Before cut: image

After cut: image

Network construction

#manually copied from "/home/osbornejr/app/output/cache/GSE68559/expression_cutoff/20/normalisation/upper_quartile/sampling/0.025/similarity/pidc/sqrt_n/threshold/0.95/threshold_method/empirical_dist_zero"
# and  output/cache/GSE68559/expression_cutoff/20/normalisation/upper_quartile/sampling/0.025/
using WGLMakie,JSServe,Markdown,Graphs,GraphMakie,NetworkLayout,JLD2,DataFrames
Page(exportable=true,offline=true)
WGLMakie.activate!()
sample_file = "_assets/menu1/sample_counts.jld2"
adj_file = "_assets/menu1/adjacency_matrix.jld2"
sample_counts = JLD2.jldopen(sample_file) do file
    file["sample counts"]
    end
pre_adj_matrix = JLD2.jldopen(adj_file) do file
    file["pre-adj_matrix"]
    end
adj_matrix = JLD2.jldopen(adj_file) do file
    file["adjacency_matrix"]
    end
components = JLD2.jldopen(adj_file) do file
    file["components"]
    end
#Trim nodes with degree zero
    network_counts = sample_counts[components[1],:][vec(sum(pre_adj_matrix,dims=2).!=0),:]
#maintain list of vertices in graph
    vertexlist = copy(network_counts[!,:transcript_type])     
g = Graph(adj_matrix)
vertex_colors = replace(vertexlist,"noncoding"=>:red,"coding"=>:blue);

begin
	set_theme!(backgroundcolor=:white)
	fig,scene,p = graphplot(g;
		layout=Spring(dim=3,C=1.0),
		node_color = vertex_colors,
		node_size = 5,
		edge_color = :grey,
		edge_width = 0.1,
		figure = (resolution = (1500, 800),)
	)
	scene.show_axis =false
	fig
end

Network analysis

Network statistics

NodesEdgesComponentsNodes in largest componentMaximal degree
24669475212466153

Type breakdown

StepCoding countsNon-coding countsNon-coding proportion
Raw counts71709327030.313
Clean counts71688326180.313
Sample counts17938160.313
Network counts16947720.313

Degree distribution

  • All nodes:

image

  • Coding transcripts:

image

  • Non-coding transcripts:

image

Hubs

Nodes with degree \(k>\bar{k}+2\sigma_{k}\):


hubs
Nodes with degree \(k>70\):

hubs

Community detection

Community 1: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0031424keratinization220.130.0026
GO:0006656phosphatidylcholine biosynthetic process220.130.0026
GO:0007399nervous system development2091813.60.0034
GO:0042127regulation of cell proliferation127148.260.0036
GO:0001649osteoblast differentiation2341.50.0059
GO:0032206positive regulation of telomere maintena...320.20.0075
GO:0070198protein localization to chromosome, telo...320.20.0075
GO:0000122negative regulation of transcription by ...4672.990.0075
GO:0019221cytokine-mediated signaling pathway3182.020.0098
GO:0030593neutrophil chemotaxis930.590.0229

Community 2: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0000165MAPK cascade5542.950.002
GO:0048011neurotrophin TRK receptor signaling path...3641.930.014
GO:0043547positive regulation of GTPase activity920.480.022
GO:0003338metanephros morphogenesis630.320.026
GO:0001823mesonephros development1330.70.026
GO:0048806genitalia development820.430.026
GO:0060054positive regulation of epithelial cell p...110.050.027
GO:0019800peptide cross-linking via chondroitin 4-...110.050.027
GO:0072287metanephric distal tubule morphogenesis110.050.027
GO:0033227dsRNA transport110.050.027

Community 3: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0033603positive regulation of dopamine secretio...220.170.0019
GO:2000065negative regulation of cortisol biosynth...220.170.0019
GO:0048484enteric nervous system development220.170.0019
GO:0032695negative regulation of interleukin-12 pr...220.170.0019
GO:0032348negative regulation of aldosterone biosy...220.170.0019
GO:0006941striated muscle contraction2141.750.0054
GO:0048485sympathetic nervous system development320.250.0056
GO:0048208COPII vesicle coating320.250.0056
GO:0018279protein N-linked glycosylation via aspar...1030.840.0078
GO:0051607defense response to virus1641.340.0102

Community 4: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0016266O-glycan processing420.270.0056
GO:0050885neuromuscular process controlling balanc...520.330.0091
GO:1900181negative regulation of protein localizat...420.270.0310
GO:0030705cytoskeleton-dependent intracellular tra...920.60.0310
GO:0008045motor neuron axon guidance110.070.0315
GO:0042245RNA repair110.070.0315
GO:0015747urate transport110.070.0315
GO:0034063stress granule assembly110.070.0315
GO:0019885antigen processing and presentation of e...110.070.0315
GO:0006982response to lipid hydroperoxide110.070.0315

Community 5: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0008150biological_process1329153203.241.2e-06
GO:0035666TRIF-dependent toll-like receptor signal...961.382.0e-05
GO:0051403stress-activated MAPK cascade2373.524.4e-05
GO:0002755MyD88-dependent toll-like receptor signa...1061.534.7e-05
GO:0034138toll-like receptor 3 signaling pathway1061.534.7e-05
GO:0034142toll-like receptor 4 signaling pathway1161.689.7e-05
GO:0034162toll-like receptor 9 signaling pathway851.220.00017
GO:0034166toll-like receptor 10 signaling pathway851.220.00017
GO:0034146toll-like receptor 5 signaling pathway851.220.00017
GO:0038123toll-like receptor TLR1:TLR2 signaling p...951.380.00035

Community 6: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0008150biological_process1329138170.810.0012
GO:0055072iron ion homeostasis1441.80.0015
GO:0001975response to amphetamine530.640.0037
GO:0006098pentose-phosphate shunt220.260.0056
GO:0033148positive regulation of intracellular est...220.260.0056
GO:0007512adult heart development220.260.0056
GO:0008272sulfate transport220.260.0056
GO:0090399replicative senescence220.260.0056
GO:0006915apoptotic process1662421.340.0098
GO:0055085transmembrane transport1201215.420.0152

Community 7: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0009235cobalamin metabolic process220.220.0037
GO:0060340positive regulation of type I interferon...220.220.0037
GO:0051988regulation of attachment of spindle micr...220.220.0037
GO:0071480cellular response to gamma radiation220.220.0037
GO:0006120mitochondrial electron transport, NADH t...730.760.0064
GO:0007059chromosome segregation1861.960.0100
GO:0045670regulation of osteoclast differentiation530.550.0104
GO:0050715positive regulation of cytokine secretio...320.330.0105
GO:0035666TRIF-dependent toll-like receptor signal...930.980.0140
GO:0048011neurotrophin TRK receptor signaling path...3663.920.0191

Community 8: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0034641cellular nitrogen compound metabolic pro...5282019.760.00049
GO:0033540fatty acid beta-oxidation using acyl-CoA...220.070.00061
GO:1901687glutathione derivative biosynthetic proc...420.150.00354
GO:0006805xenobiotic metabolic process1630.60.00648
GO:0044281small molecule metabolic process239128.940.00695
GO:0014047glutamate secretion820.30.01549
GO:0007283spermatogenesis4041.50.01607
GO:0032504multicellular organism reproduction6062.250.02297
GO:0070564positive regulation of vitamin D recepto...110.040.02495
GO:0060391positive regulation of SMAD protein sign...110.040.02495

Community 9: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0055085transmembrane transport120128.390.0035
GO:0007596blood coagulation5263.640.0038
GO:0035999tetrahydrofolate interconversion320.210.0044
GO:0006357regulation of transcription by RNA polym...12668.810.0119
GO:0007269neurotransmitter secretion1631.120.0137
GO:0032781positive regulation of ATPase activity520.350.0139
GO:0030049muscle filament sliding520.350.0139
GO:0001523retinoid metabolic process520.350.0139
GO:0051384response to glucocorticoid1531.050.0185
GO:0042476odontogenesis1941.330.0196

Community 10: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0008219cell death1842929.932.3e-06
GO:0008150biological_process1329166216.213.8e-05
GO:0006355regulation of transcription, DNA-templat...2883946.850.00034
GO:0051402neuron apoptotic process2954.720.00269
GO:0007268chemical synaptic transmission711411.550.00779
GO:0034501protein localization to kinetochore220.330.00806
GO:0021554optic nerve development220.330.00806
GO:0032463negative regulation of protein homooligo...220.330.00806
GO:0007080mitotic metaphase plate congression220.330.00806
GO:0015701bicarbonate transport220.330.00806

Community 11: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0010881regulation of cardiac muscle contraction...630.420.00089
GO:0007603phototransduction, visible light630.420.00131
GO:0048205COPI coating of Golgi vesicle220.140.00134
GO:0006890retrograde vesicle-mediated transport, G...320.210.00393
GO:0006891intra-Golgi vesicle-mediated transport320.210.00393
GO:0002027regulation of heart rate1440.970.00617
GO:0086064cell communication by electrical couplin...630.420.00746
GO:0070933histone H4 deacetylation420.280.00766
GO:0051384response to glucocorticoid1541.040.01013
GO:0001523retinoid metabolic process520.350.01247

Community 12: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0040015negative regulation of multicellular org...220.080.00051
GO:0051291protein heterooligomerization420.170.00295
GO:0007601visual perception1430.580.00336
GO:0007568aging2441.00.00391
GO:0060314regulation of ryanodine-sensitive calciu...720.290.00989
GO:0008217regulation of blood pressure2140.880.01519
GO:0051603proteolysis involved in cellular protein...4031.670.02216
GO:0034616response to laminar fluid shear stress220.080.02225
GO:0000302response to reactive oxygen species1720.710.02243
GO:0007352zygotic specification of dorsal/ventral ...110.040.02278

Community 13: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0006099tricarboxylic acid cycle320.250.0057
GO:0035999tetrahydrofolate interconversion320.250.0057
GO:0030514negative regulation of BMP signaling pat...420.330.0111
GO:0007399nervous system development2091517.110.0126
GO:0001707mesoderm formation520.410.0179
GO:0008542visual learning620.490.0261
GO:0045668negative regulation of osteoblast differ...720.570.0355
GO:0008360regulation of cell shape1731.390.0367
GO:0006367transcription initiation from RNA polyme...1731.390.0367
GO:0050793regulation of developmental process1691513.840.0406

Community 14: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0008150biological_process1329165232.073.8e-05
GO:0006511ubiquitin-dependent protein catabolic pr...36106.290.00022
GO:0072659protein localization to plasma membrane741.220.00070
GO:0007218neuropeptide signaling pathway1352.270.00384
GO:0007267cell-cell signaling1261822.00.00437
GO:0007166cell surface receptor signaling pathway2152837.540.00693
GO:0071108protein K48-linked deubiquitination220.350.00796
GO:0042572retinol metabolic process220.350.00796
GO:0045672positive regulation of osteoclast differ...220.350.00796
GO:0030422production of siRNA involved in RNA inte...220.350.00796

Community 15: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0008150biological_process13294759.820.0012
GO:0042059negative regulation of epidermal growth ...320.140.0019
GO:0000278mitotic cell cycle8243.690.0249
GO:0042228interleukin-8 biosynthetic process220.090.0250
GO:0042267natural killer cell mediated cytotoxicit...420.180.0250
GO:0002495antigen processing and presentation of p...1620.720.0252
GO:0030382sperm mitochondrion organization110.050.0255
GO:0048240sperm capacitation110.050.0255
GO:0042245RNA repair110.050.0255
GO:1900017positive regulation of cytokine producti...110.050.0255

Community 16: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0071280cellular response to copper ion220.20.0023
GO:0043691reverse cholesterol transport220.20.0023
GO:0006359regulation of transcription by RNA polym...320.290.0067
GO:0048013ephrin receptor signaling pathway420.390.0130
GO:0035329hippo signaling420.390.0130
GO:0010951negative regulation of endopeptidase act...1241.180.0202
GO:0008219cell death1841318.060.0206
GO:0090263positive regulation of canonical Wnt sig...520.490.0209
GO:0007218neuropeptide signaling pathway1331.280.0219
GO:0033138positive regulation of peptidyl-serine p...620.590.0304

Community 17: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0070098chemokine-mediated signaling pathway320.080.0010
GO:0006367transcription initiation from RNA polyme...1730.470.0036
GO:0001570vasculogenesis620.170.0050
GO:0045669positive regulation of osteoblast differ...620.170.0050
GO:0035690cellular response to drug2240.610.0061
GO:0060021roof of mouth development820.220.0091
GO:0001958endochondral ossification820.220.0091
GO:0010761fibroblast migration420.110.0185
GO:0003143embryonic heart tube morphogenesis720.190.0185
GO:0060548negative regulation of cell death8132.240.0187

Community 18: Go annotation terms:

GO_IDTermAnnotatedSignificantExpectedfisher
GO:0006112energy reserve metabolic process2072.280.0013
GO:0048266behavioral response to pain530.570.0024
GO:0045672positive regulation of osteoclast differ...220.230.0042
GO:0010940positive regulation of necrotic cell dea...220.230.0042
GO:0051497negative regulation of stress fiber asse...220.230.0042
GO:0051056regulation of small GTPase mediated sign...3974.440.0045
GO:2000134negative regulation of G1/S transition o...1341.480.0118
GO:0019933cAMP-mediated signaling830.910.0119
GO:0071294cellular response to zinc ion320.340.0121
GO:0048873homeostasis of number of cells within a ...320.340.0121

3D visualisation

Graphlet counting

Comparing the typed representations of different graphlets in the real network to a set of networks with the same structure, but randomised node types.

  • Tables

hubs
Graphlet Expected Observed
coding_noncoding_edge 1664.31 1690
coding_coding_edge 18184.0 18149
noncoding_noncoding_edge 36.72 46
hubs
Graphlet Expected Observed
coding_coding_noncoding_3-path 21473.3 18915
coding_noncoding_noncoding_3-path 997.68 547
noncoding_coding_noncoding_3-path 480.34 356
coding_noncoding_coding_3-path 11246.4 7095
coding_coding_coding_3-path 2.37068e5 244366
noncoding_noncoding_noncoding_3-path 21.38 8
hubs
Graphlet Expected Observed
coding_noncoding_noncoding_3-tri 893.66 2052
coding_coding_noncoding_3-tri 19884.7 25026
coding_coding_coding_3-tri 1.41849e5 135501
noncoding_noncoding_noncoding_3-tri 13.0 61
hubs
Graphlet Expected Observed
noncoding_coding_coding_noncoding_4-path 7078.75 5911
coding_coding_coding_coding_4-path 3.42802e6 3561835
coding_coding_noncoding_coding_4-path 3.21663e5 219004
coding_coding_coding_noncoding_4-path 3.12688e5 299825
coding_noncoding_noncoding_coding_4-path 7209.26 3529
noncoding_coding_noncoding_noncoding_4-path 640.79 292
coding_coding_noncoding_noncoding_4-path 14248.7 9301
coding_noncoding_noncoding_noncoding_4-path 632.32 97
noncoding_coding_noncoding_coding_4-path 14316.5 6719
noncoding_noncoding_noncoding_noncoding_4-path 14.33 0
hubs
Graphlet Expected Observed
coding_coding_coding_noncoding_4-star 2.43116e5 206162
coding_coding_noncoding_coding_4-star 88314.3 50863
coding_noncoding_coding_noncoding_4-star 10829.5 6930
noncoding_noncoding_coding_noncoding_4-star 157.66 72
noncoding_noncoding_noncoding_noncoding_4-star 6.83 2
coding_coding_coding_coding_4-star 1.80134e6 1885477
coding_noncoding_noncoding_noncoding_4-star 511.03 200
coding_coding_noncoding_noncoding_4-star 11865.7 6439
hubs
Graphlet Expected Observed
coding_coding_noncoding_coding_4-tail 1.67961e5 94217
coding_coding_noncoding_noncoding_4-tail 7432.14 3735
coding_noncoding_noncoding_noncoding_4-tail 645.87 230
coding_coding_coding_coding_4-tail 3.54037e6 3664555
noncoding_noncoding_coding_coding_4-tail 6861.39 7372
coding_coding_coding_noncoding_4-tail 1.59608e5 141300
coding_noncoding_coding_noncoding_4-tail 14438.6 12601
noncoding_noncoding_noncoding_coding_4-tail 327.28 220
noncoding_noncoding_coding_noncoding_4-tail 307.19 349
noncoding_noncoding_noncoding_noncoding_4-tail 13.95 5
coding_noncoding_noncoding_coding_4-tail 14946.7 7308
coding_noncoding_coding_coding_4-tail 3.21477e5 302500
hubs
Graphlet Expected Observed
coding_coding_coding_noncoding_4-cycle 2980.68 1613
coding_coding_noncoding_noncoding_4-cycle 200.78 50
coding_coding_coding_coding_4-cycle 15564.5 17089
coding_noncoding_noncoding_noncoding_4-cycle 5.98 0
noncoding_noncoding_noncoding_noncoding_4-cycle 0.08 0
hubs
Graphlet Expected Observed
coding_noncoding_noncoding_noncoding_4-chord 50.53 24
coding_coding_coding_noncoding_4-chord 24504.8 14353
coding_coding_noncoding_coding_4-chord 24458.5 25984
coding_noncoding_noncoding_coding_4-chord 516.48 1392
noncoding_coding_noncoding_noncoding_4-chord 43.11 1
noncoding_coding_coding_noncoding_4-chord 536.98 76
coding_coding_coding_coding_4-chord 256059.0 265812
coding_coding_noncoding_noncoding_4-chord 2262.62 791
noncoding_noncoding_noncoding_noncoding_4-chord 0.96 0
hubs
Graphlet Expected Observed
coding_coding_noncoding_noncoding_4-clique 15039.5 54411
coding_coding_coding_coding_4-clique 1.12363e6 956621
coding_coding_coding_noncoding_4-clique 2.16407e5 340872
noncoding_noncoding_noncoding_noncoding_4-clique 4.83 71
coding_noncoding_noncoding_noncoding_4-clique 446.83 3553
  • Boxplots

hubs
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Significantly overrepresented type representations

Graphlet Expected Observed p_value
3.63e+05 407182 0.014
7.63e+04 91582 0.02
4.32e+05 520126 0.000999
3.89e+06 4334911 0.000999
3.07e+06 3678945 0.000999
    coding     noncoding
Graphlet Expected Observed p_value
3.82e+04 50002 0.000999
6.82e+06 7731136 0.000999
1.21e+06 1266163 0.045
2.87e+06 3043339 0.00699
5.74e+06 6197411 0.002
    coding     noncoding
Graphlet Expected Observed p_value
9.86e+06 12166548 0.000999
8.3e+06 9152303 0.000999
3.77e+05 395016 0.000999
4.48e+05 512660 0.000999
1.34e+05 140140 0.049
 



 

Significantly underrepresented type representations

Graphlet Expected Observed p_value
3.62e+05 322980 0.00799
6.39e+04 38106 0.002
7.6e+04 48906 0.000999
1.34e+04 8702 0.00999
3.05e+05 257529 0.002
    coding     noncoding
Graphlet Expected Observed p_value
1.29e+06 924441 0.000999
9.55e+04 61509 0.000999
6.84e+05 451034 0.000999
1.63e+06 1115851 0.000999
1.13e+04 6890 0.000999
    coding     noncoding
Graphlet Expected Observed p_value
1.19e+03 570 0.002
2.7e+04 21890 0.003
1.35e+04 10893 0.003
2.86e+06 2362480 0.000999
1.21e+06 934594 0.000999
    coding     noncoding
Graphlet Expected Observed p_value
1.01e+06 776743 0.003
5.06e+05 408876 0.00599
2.12e+05 164238 0.00799
2.41e+06 1946136 0.002
8.28e+06 7800810 0.000999
    coding     noncoding
Graphlet Expected Observed p_value
1.74e+06 1248873 0.000999
3.48e+06 2965677 0.000999
1.46e+06 1082325 0.000999
3.05e+05 167719 0.000999
3.48e+06 2894790 0.000999
    coding     noncoding
Graphlet Expected Observed p_value
1.46e+06 928259 0.000999
1.58e+05 120156 0.000999
1.88e+05 156055 0.000999
3.32e+04 23411 0.002